Less than two years after taking the job, Southampton Town Police Chief William Wilson submitted his resignation today, effective Dec. 1.

Chief Wilson was hired in May 2011 to replace longtime police chief James Overton, who retired after 21 years on the job. Chief Wilson had previously been chief of the Southampton Village police department for five years.

But his short tenure as town chief was marked by battles with the Town Board over funding and staffing issues, as well as investigations into alleged wrongdoing within the department.

The chief has complained that his department is understaffed, which had resulted in an increase in overtime costs as well as the elimination of a second sector car in the Flanders-Riverside area.

The Southampton Town Board recently voted to approve a settlement that reinstated Lieutenant James Kiernan, who had been suspended based on charges brought by Chief Wilson, since May 4, 2012.

The Suffolk County District Attorney’s office has also reportedly investigated incidents that took place before Chief Wilson took the helm at the town department, involving missing documents and members of the department’s Street Crime Unit, which Chief Wilson disbanded when he took over.

Chief Wilson also had the town department join the district attorney’s East End Drug Task Force, something his predecessor never did.

Southampton Supervisor Anna Throne-Holst issued a statement Tuesday saying that she respects the chief’s decision to leave and “will do my utmost to insure a seamless and positive transition.”

“I also share Chief Wilson’s concern with regard to proper staffing levels and the need for the implementation of modern police technologies, which have been and remain a priority for me,” she said.

“I have confidence the current management at the Southampton Police Department will work together with us, the Town Board, and their fellow police officers, toward an effective transition,” she added. “In the next few days, I will be conferring with my fellow Town Board members to develop a transition plan and a proactive course leading to the next phase of leadership for the Police Department.

“Again, I thank Chief Wilson for his service to the town and wish him the very best.”